Started by upstream project "BIOFORMATS-test-repo" build number 270 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7370938582346606114.sh + '[' leica = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42595_merge_ci -v /uod/idr/repos/curated/leica:/data -v /uod/idr-scratch/merge-ci/curated/leica:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 11:36:34,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:36:34,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 11:36:34,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:36:34,896 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:36:34,896 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:36:34,897 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:36:34,897 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:36:34,897 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:36:34,897 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:36:34,898 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:36:34,898 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:36:34,898 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:36:35,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:36:35,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:36:35,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:36:35,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:36:35,214 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:36:35,214 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:36:35,214 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:36:35,215 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:36:35,215 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 11:36:35,215 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 11:36:35,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 319 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 11:36:35,224] [main] java.version = 17.0.2 [testng] 11:36:35,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:36:35,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:35,389 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_11-36-35.log] [testng] 11:36:35,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 11:36:35,450] [main] testng.directory = /data [testng] [2024-11-27 11:36:35,451] [main] testng.configDirectory = /config [testng] [2024-11-27 11:36:35,846] [main] testng.multiplier = 1.0 [testng] [2024-11-27 11:36:35,847] [main] testng.in-memory = false [testng] [2024-11-27 11:36:35,848] [main] testng.allow-missing = false [testng] [2024-11-27 11:36:35,848] [main] user.language = en [testng] [2024-11-27 11:36:35,848] [main] user.country = ${user.country} [testng] [2024-11-27 11:36:35,848] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 11:37:36,573] [main] ---------------------------------------- [testng] [2024-11-27 11:37:36,574] [main] Total files: 5651 [testng] [2024-11-27 11:37:36,574] [main] Scan time: 60.725 s (10 ms/file) [testng] [2024-11-27 11:37:36,574] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 11:39:19,077] [pool-1-thread-1] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 11:39:19,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:39:19,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:19,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_11-39-19.log] [testng] 11:39:19,079 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51c48fb2 - End of configuration. [testng] [2024-11-27 11:39:20,630] [pool-1-thread-12] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 11:39:20,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:39:20,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:20,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_11-39-20.log] [testng] 11:39:20,631 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ad4e089 - End of configuration. [testng] [2024-11-27 11:39:21,449] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 11:39:21,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:39:21,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:21,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_11-39-21.log] [testng] 11:39:21,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12389cda - End of configuration. [testng] [2024-11-27 11:39:22,119] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 11:39:22,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:39:22,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:22,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_11-39-22.log] [testng] 11:39:22,120 |-INFO in ch.qos.logback.core.sift.SiftProcessor@435f1078 - End of configuration. [testng] [2024-11-27 11:39:22,891] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei: [testng] 11:39:22,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:39:22,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:22,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_11-39-22.log] [testng] 11:39:22,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9793490 - End of configuration. [testng] [2024-11-27 11:39:23,559] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 11:39:23,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:39:23,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:23,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_11-39-23.log] [testng] 11:39:23,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66881f48 - End of configuration. [testng] [2024-11-27 11:39:27,238] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] 11:39:27,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:39:27,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:27,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_11-39-27.log] [testng] 11:39:27,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7279b0de - End of configuration. [testng] [2024-11-27 11:39:28,412] [pool-1-thread-6] Initializing /data/julie/biorad/25-65.tif: [testng] 11:39:28,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:39:28,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:28,412 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_11-39-28.log] [testng] 11:39:28,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cdedf84 - End of configuration. [testng] [2024-11-27 11:39:29,090] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 11:39:29,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:39:29,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:29,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_11-39-29.log] [testng] 11:39:29,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2df6a575 - End of configuration. [testng] [2024-11-27 11:39:29,146] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 11:39:29,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:39:29,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:29,146 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_11-39-29.log] [testng] 11:39:29,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b66a86a - End of configuration. [testng] [2024-11-27 11:39:29,191] [pool-1-thread-3] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 11:39:29,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:39:29,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:29,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_11-39-29.log] [testng] 11:39:29,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ee5ebbd - End of configuration. [testng] [2024-11-27 11:39:29,575] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 11:39:29,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:39:29,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:29,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_11-39-29.log] [testng] 11:39:29,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@509b8cbd - End of configuration. [testng] [2024-11-27 11:39:34,895] [pool-1-thread-4] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-11-27 11:39:35,141] [pool-1-thread-5] Initializing /data/oliver/o459/o459.lei: [testng] [2024-11-27 11:39:41,534] [pool-1-thread-4] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-11-27 11:39:44,757] [pool-1-thread-6] Initializing /data/julie/c164_1.tif: [testng] [2024-11-27 11:39:52,373] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-11-27 11:39:53,584] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-11-27 11:39:55,462] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-11-27 11:39:56,449] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-11-27 11:39:58,329] [pool-1-thread-6] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-11-27 11:40:01,515] [pool-1-thread-2] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-11-27 11:42:47,145] [pool-1-thread-11] Initializing /data/david/intestine/intestine.lei: [testng] [2024-11-27 11:43:06,234] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-11-27 11:43:12,199] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-11-27 11:43:31,010] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-11-27 11:45:14,001] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei: [testng] [2024-11-27 11:45:28,564] [pool-1-thread-10] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-11-27 11:46:27,735] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-11-27 11:47:22,528] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: Build was aborted Calling Pipeline was cancelled Finished: ABORTED